Answer for How to set up the folders when merging Kodi Steaming Add-ons into a video library that is spit out on different NAS drives?

You may want to check out this most https://kinkeadtech.com/2015/09/add-shows-to-kodi-genesis-from-any-htpc-in-the-house/ which answers your question about changing the location of the Genesis stream library files.  This would allow you to select a NAS location.
 
Regarding merging separate plugin sources with your stored media files, Kodi just has you add all those as separate video sources, and they get merged automatically in the library.  However, I’ve seen it happen before where each episode in a show is duplicated.